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Table of Contents

Introduction

CLASHChimeras is a Python package for analysing CLASH datasets. It takes raw fastq files as input and provides comprehensive analysis of RNA profiles and chimeric reads identification. The output is CSV and BED format files for easy visualization in Genome Browsers.

Dependencies

CLASHChimeras requires certain software to be installed and setup before you can use it completely. The software you need to explicitly install are the following:

  • Bowtie2 - Fast and sensitive read alignment
  • Tophat - A spliced read mapper for RNA-Seq

Usage

The package can be used by three executable scripts

  1. download-for-chimeras
  2. align-for-chimeras
  3. find-chimeras

download-for-chimeras

$ download-for-chimeras -gor "H.sapiens" -mor hsa

Downloads required sequences and create bowtie2 indexes required for alignment

align-for-chimeras

$ align-for-chimeras -i input.fastq -si /path/to/database -ti
/path/to/database
 -o output

Given a fastq file, this script executes bowtie2 and tophat aligners to generate alignment files necessary for detecting chimeras in the reads

find-chimeras

$ find-chimeras -s smallRNA.sam -t targetRNA.sam -o output

Given two SAM files, this script tries to find chimeras that are observed between a smallRNA and a targetRNA

Check out the documentation for installation instructions and detailed usage with example